First of all, this article shows that Behe's work has indeed contributed to
science. Thornhill and Ussery (T&U) write:

"However, the more theoretical question about the accessibility by Darwinian
evolution of irreducibly complex structures of functionally indivisible components,
if such exist, has not been thoroughly examined. ….One factor hampering examination
of the accessibility of biological structures by Darwinian evolution is the
absence of a classification of possible routes. A suggested classification
is presented here."

Although one can argue about it, this can be viewed as a fundamental confirmation
of Behe's thesis that the origin of these IC structures has not been explained
by science. However, what should be clear is that Behe's skepticism has served
as an impetus for these scientists to develop a classification that did not
exist before. Therefore, Behe has indeed contributed in an indirect way by serving
as the stimulus for the creation of such a classification.

T&U then define terms, but strangely, do not use Behe's definition of IC.
Of interest also is their definition of Darwinian evolution. It includes the
following: "no intervention by conscious agent(s) occurs." Once again, we see
how an a priori assumption of science works to exclude a teleological
cause (reminding us that science is simply not an authority when dealing with
question of teleology vs. non-teleology).

T&U then outline the four possible routes of Darwinian evolution.

The first is: Serial direct Darwinian evolution. This means change
along a single axis.

Here again we get to see the contribution of Behe as the authors then note,
"Although it can generate complicated structures, it cannot generate irreducibly
complex structures."

So we can see that IC helps to rule out certain evolutionary pathways. This
is also very significant in that the most persuasive examples of random mutation
and natural selection (RM&NS) entail serial direct Darwinian evolution. The
traditional examples of Darwin's finches (and their beaks), giraffe necks, elephant
trunks, darkening wings in moths are all examples of serial direct Darwinian
evolution. Thus, this means that evidence for this type of evolution is not
evidence that IC can/did evolve via the blind watchmaker mechanism (BWM).

The second mechanism is: Parallel direct Darwinian evolution. This
means approximately synchronous changes in more than one component, so that
modification to other components always occurs before the total modification
to any one component has become significant.

They then cite some examples:

Most complex supramolecular biological structures have primarily this type
of accessibility by Darwinian evolution, with examples being bat echolocation,
spiders' web construction, honeybee waggle dances, and insect mimicry by orchids
(Dawkins, 1986, 1995). Some complex (but not irreducibly complex) molecular
systems, such as the globin proteins (Ptitsyn, 1999; Satoh, 1999), could also
have evolved in this manner.

But they also write:

Parallel direct Darwinian evolution can generate irreducibly complex structures,
but not irreducibly complex structures of functionally indivisible components,
and this is the valid conclusion to draw from Behe's thesis.

Thus, once again, we can see that when we are dealing with IC molecular machines
(which are composed of functionally indivisible parts), the various examples
of Darwinian evolution cited by Dawkins et al. are irrelevant. None of it amounts
to evidence that Behe's IC examples evolved by the BWM.

Thus, before we go on, let's consider that despite all the expressed incredulity
that is so common among Behe's critics, he has indeed contributed to science
by forcing scientists to classify routes of evolution and by showing that 50%
of the possible routes can't generate IC machines. This is progress. Without
Behe, for example, many would probably still think that classic evidence of
RM&NS allows us to think that the bacterial flagellum evolved by the same mechanism.

Next, we turn to the remaining two possible routes in which Darwinian evolution
(DE) can generate IC, that of Elimination of functional redundancy and
Adoption from a different function. The authors use the analogy of an
arch to illustrate how these mechanisms might work to generate IC:

"The arch is irreducibly complex, and, assuming that cement does not
set instantaneously, any arch one sees must therefore either have been built
using scaffolding, analogously to redundancy elimination, or have been built
elsewhere, perhaps horizontally, and moved into position when the cement had
set, analogously to adoption."

The biological examples used by the authors to support these mechanisms are
not very impressive, as the authors shy away from addressing any of Behe's examples
in detail. In the case of functional redundancy, the authors spend most their
time on the origin of the mammalian jaw and not a molecular machine. When it
comes to the adoption from a different function, the authors write of the origin
of feathers from scales, shared domains in different proteins, and two examples
where a protein has been co-opted to perform an alternative function (i.e.,
crystallins). Let's take a closer look at the two possible Darwinian pathways
for generating IC.

Adoption from a Different Function

Ironically, the main problem with this pathway was first highlighted by another
Behe-critic, H. Allen Orr. In his critique from Boston Review, Orr writes:

"First it will do no good to suggest that all the required parts of
some biochemical pathway popped up simultaneously by mutation. Although this
"solution" yields a functioning system in one fell swoop, it's so hopelessly
unlikely that no Darwinian takes it seriously. As Behe rightly says, we gain
nothing by replacing a problem with a miracle. Second, we might think that
some of the parts of an irreducibly complex system evolved step by step for
some other purpose and were then recruited wholesale to a new function. But
this is also unlikely. You may as well hope that half your car's transmission
will suddenly help out in the airbag department. Such things might happen
very, very rarely, but they surely do not offer a general solution to irreducible
complexity."

To appreciate why co-option is unlikely to be a general solution to IC, let's
return to Behe's definition of IC:

"By irreducibly complex I mean a single system composed of several well-matched,
interacting parts that contribute to the basic function, wherein the removal
of any one of the parts causes the system to effectively cease functioning."

and

"An irreducibly complex system is one that requires several closely matched
parts in order to function and where removal of one of the components effectively
causes the system to cease functioning."

Since an IC system is built from closely/well-matched parts, it is unlikely
that a component shaped to fulfill another function can snuggly plug-in to generate
the IC function. In fact, Behe anticipates this solution by writing:

"Even if a system is irreducibly complex (and thus cannot have been
produced directly), however, one cannot definitively rule out the possibility
of an indirect, circuitous route. As the complexity of the an interacting
system increases, though, the likelihood of such an indirect route drops precipitously."

To illustrate this point, let's consider the bacterial flagellum (perhaps
the most well known example of an IC system). A functioning flagellum requires
about 30 gene products (components). So what does the co-option hypothesis predict?
That prior to the existence of the flagellum, these 30 gene products (or their
duplicates) all existed doing something else. Then, they just happened to all
fit together by chance to create a flagellum. And afterwards, the other 30 or
so hypothetical functions of these original gene products disappeared. Does
this really sound like a general solution to IC?

The brilliance of Darwin was to minimize the role of chance in apparent design.
But once we turn to the co-option explanation, we leave this explanatory appeal
behind, as chance reasserts itself into a place of prominence. For it is chance
that determines whether the 30-or-so gene products just happen to come together
to form a functioning flagellum, as selection was pruning these gene products
in accord with 30-or-so different functions. Thus, the co-option explanation
is really a return to using chance as an explanation for apparent design, and
just as it was not convincing in pre-Darwinian days, it is not convincing today.

One seeming way around this problem is to imagine 5 or 6 subsystems, each
composed of 6 or 5 gene products, all conducting different functions. Thus,
we need only imagine that by chance, 5 or 6 subsystems could happen to come
together to form a well-matched whole that generates a new function. But I don't
see how this helps much as Orr's critique still applies. And what's worse, in
this case, the non-teleologist must now explain the origin of 5 or 6 different
IC systems and why they too disappeared after the origin of the new IC system.

When we return to the T&U paper, this problem becomes obvious as the examples
of adoption that the authors list give us no reason to think IC system arose
by this pathway. Their first example is that of the transition from scales to
feathers. But it is not clear this is an example of generating IC and this whole
topic ignores Behe's points on pp. 40-41. The fact that various proteins can
share domains doesn't really support adoption from a different function, as
there is no reason to think a designer would ensure that each and every part
of a system is truly unique. For example, that both a lawnmower and automobile
have spark plugs is not evidence that one motor was co-opted to form another
by random changes and selection.

The only clear examples, in in my opinion, of adoption from a different function
are as follows:

Antifreeze glycoprotein in the blood of Antarctic notothenioid fishes,
which enables them to survive in icy seas, is considered to have evolved from
a functionally unrelated pancreatic trypsinogen-like protease, and the recent
discovery of chimeric genes which encode both the protease and an antifreeze
glycoprotein polyprotein strongly supports this theory (Cheng & Chen, 1999).

Crystallins (proteins with refractive functions in the eye lens) are
closely related or identical to stress-protective proteins in non-ocular tissues
(eg. Drosophila a-crystallins and small heat-shock proteins are homologous).

But note that in both cases, these proteins don't function as well-matched
components in an IC system. Thus, while sometimes a protein might adopt a different
function since it is not constrained to interact with multiple partners, an
IC component is unlikely to arise in this fashion because it is constrained
to interact with multiple partners.

Since the adoption from a different function explanation relies heavily on
pure chance, it is unlikely to be a general solution to IC. In fact, as Behe
notes, the more complex the system, the less likely that this pathway is what
generated IC (since it relies more heavily on converging independent, random
events).

But there is another problem with the adoption explanation. To illustrate
this, let's use a simple 3-part IC system, the chaperone machine. The chaperone
machine is a protein complex that binds proteins in their partially unfolded
state to prevent aggregation in the cell. Each of the three parts fulfills a
different role. DnaK is the protein clamp that binds to other proteins. DnaJ
is the protein that loads the clamp. And GrpE is the protein that unloads the
clamp (the mechanism is more complicated and involves coordinated movement tied
to ATP hydrolysis, but this simple description will suffice).

What the adoption explanation assumes is an inherently flexibility/plasticity
to IC components. And what this assumption thus predicts is permutations. That
is, IC systems should demonstrate much variability. We should see some bacteria
with dnaK and two other chaperones (not dnaJ and grpE). We should see others
with dnaJ and two other proteins (not dnaK and grpE). We should also see some
bacteria with grpE (and not dnaK and grpE). But we don't. For example, imagine
a mutation occurred in a bacterium that disabled dnaJ. IC predicts this would
be lethal and selection would prevent this organism from altering the gene pool.
But if adoption from a different function is common, the mutation need not be
lethal and a new chaperone machine would evolve around the protein substituting
for the lost component.

When we look to eubacteria, the three chaperone components are universal.
They are found in gm+ and gm- bacteria, thermophiles (Thermotoga and Aquifex),
spirochetes, Deinococcus, Campylobacter, cyanobacteria, Neisseria, and even
Mycoplasma. Again, this is most likely due to the fact that this chaperone machine
is IC (IC predicts functional constraint) and other proteins cannot substitute
through adoption from a different function.

Recently, it was determined that most known Archaea lack this chaperone machine.
That some have it has been attributed to horizontal transfer. Here was a good
opportunity to gather more positive support for the IC status of such an ancient
and highly conserved system. I predicted that where we would find the chaperone
machine in Archaea, we'd find all three components given that it is IC. Then,
not too long ago, I came across a review paper on stress genes and proteins
that verified this prediction. The authors noted that genomic data demonstrate
the following in Archea:

"whenever hsp70 was present in a genome, hsp40 and grpE were also found
if enough sequencing was done; conversely, genome sequencing has demonstrated
that if the hsp70 gene is absent, hsp40 and grpE are also absent."

IC nicely explains this as the lateral transfer of only one or two components
of the chaperone machine would be useless and thus degrade. That's why you see
either all three gene products or none. But if adoption from a different function
was a common IC generator, we should see permutations in Archaea, where a laterally
transferred dnaK gene would find helpers in the archaeal cytoplasm and evolve
a new chaperone machine. And all of this is significant because the chaperone
machine is a very simple example of IC having only three parts.

Thus, it would seem that the more complex an IC system is, and the less variable
it is across phylogenetic lines, the less likely it is that adoption from a
different function explains its origin.

One last problem with the adoption explanation is that it ignores another
element of Behe's argument (pp. 43-45):

"To feel the full force of the conclusion that a system is irreducibly complex
and therefore has no functional precursors, we need to distinguish between
a physical precursor and a conceptual precursor. . . . Darwinian evolution
requires physical precursors."

That is, Darwinian evolution is supposed to be a description of history. Thus,
it invokes real-life proteins with real functions that are really co-opted into
a conglomerate to perform a new, real function. Darwinists tend to overlook
this and prefer to remain in the conceptual realm, where proteins are imagined
to have unknown functions such that they somehow get adopted into another conglomerate.
And that's where it all ends with most Darwinists. But as Behe notes, we need
physical precursors and this means we need evidence of these physical precursors.
Thus, unless the adoption from a different function story is supported by real
evidence, it fails to explain the origin of the IC system.

In summary, the adoption from a different function explanation is unlikely
to be a general solution to IC (as Orr notes) as it relies too heavily on pure
chance as an explanation for apparent design. We thus need independent evidence
that this explanation validly applies in any system in question, especially
in light of the fact that examples of this pathway do not lend themselves easily
to explaining the origin of IC. Furthermore, if we don't see evidence of permutations
that run through out the entire IC system, there is good reason to dismiss this
explanation. So let's turn our attention to the remaining Darwinian pathway.

Elimination of Function Redundancy

The interesting thing about this pathway is that it too robs the standard
Darwinian explanation of its appeal. Richard Dawkins presents Darwinism in its
most convincing form:

"We have seen that living things are too improbable and too beautifully
'designed' to have come into existence by chance. How, then, did they come
into existence? The answer, Darwin's answer, is by gradual, step- by-step
transformations from simple beginnings, from primordial entities sufficiently
simple to have come into existence by chance."

Yet elimination of function redundancy is an explanation that does not begin
with "simple beginnings," but instead begins with a state that is more complex
than that which is observed. But if simple beginnings are needed to "come into
existence by chance," the complicated beginning, assumed by this pathway, may
be too complicated to "come into existence by chance."

It seems to me that this pathway is not taken seriously when it comes to explaining
origins through non-teleological mechanisms. For example, another Behe-critic,
Clare Stevens, relies on simple (more direct) beginnings to explain the origin
of IC:

"So how can the whole process have arisen step by step as required
by gradual evolution? It certainly is impossible to believe that these complex
sequential processes arose all at once. So we must look for a different format.
For a start we must assume that there was a more direct method of synthesis
available at one stage indeed that a more direct process might still be available
in some creature yet to be investigated (as I have suggested in the case of
adenine). Then we must go on to surmise that the intermediate stages are refinements
interpolated subsequently."

In fact, even Ussery himself (one of the authors of the paper) uses simple
beginnings on his web page to explain the origin of the bacterial flagellum:

"If you look at bacterial flagella, you find that some are indeed quite
complicated, but others are more simple. For example, the basal body can vary
with species - in E. coli there are four rings, in Bacillus subtilis two rings,
and in Caulobacter crescentus five rings. I can easily imagine a scenario
where a "primitive bacterium" might have one ring, and then you have a flagellum
with two rings, then three, and so on. This is a "gradual, step-by-step" evolution,
which is the antithesis of Behe's argument."

"It is likely that as new bacterial genomes continue to be sequenced (at
the rate of about one a month!), organisms will be found which require even
fewer genes to make a completely functional flagella."

Thus, Dawkins, Stevens, and Ussery (and many more) all go back to "simple
beginnings," the very opposite initial state assumed by this pathway.

However, I personally find this pathway of redundancy elimination to be very
interesting, as it may suggest that some originally designed states were much
more complex than seen today, such that evolution was essentially rigged to
evolve in particular directions. In other words, this pathway does not eliminate
the design inference behind IC, but instead, suggests that IC is an indirect
indicator of an originally designed state.

Nevertheless, what we need is evidence that the initial state was more complicated
than the IC state. For example, are we talking about flagellum that were originally
composed of 60 parts? Where is the evidence for such a claim? It is an interesting
thought, but without evidence, we can't take it beyond the realm of philosophy.

Conclusions

Behe's notion of IC has found itself into the scientific literature and is
being taken seriously by scientists. Behe has contributed to science by forcing
non-teleologists to once-and-for-all lay the various Darwinian pathways on the
table. This is progress as we can now look to the data to determine if there
is any evidence that these pathways apply to an particular IC system in question.

Behe's notion of IC does indeed help us to effectively rule out some of the
Darwinian pathways, as admitted by T&U. What is most relevant is that the pathways
ruled out by IC are also those best supported by example/evidence and those
that are most persuasive in explaining apparent design. The traditional examples
of Darwin's finches (and their beaks), giraffe necks, elephant trunks, antibiotic
resistance, and the darkening wings in moths give us no reason to think IC systems
were generated by the RM&NS. The remaining explanations for IC are indeed possible,
but without evidence to support them, there is no reason to seriously embrace
them. Neither explanation constitutes a better general solution to IC than intelligent
design. What's more, both explanations seriously weaken the overall appeal of
the standard non-teleological explanations, as they resurrect a prominent role
for pure chance in the origin of apparent design and/or rely on complicated
initial states that may lend themselves more readily to a teleological cause.